Re: [ccp4bb] cns and refmac refinement

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008

Previous message:
Subject: cns and refmac refinement
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-02-21

Next message:
Subject: Re: Vista
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-21

Subject: Re: cns and refmac refinement
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-02-21

Hi Yang Li,

trying alternatives is always good thing to do -:)

If you have latest PHENIX installed, try this:

% phenix.refine model.pdb data.mtz
strategy=rigid_body+individual_sites+individual_adp
simulated_annealing=true optimize_wxc=true optimize_wxu=true
main.number_of_macro_cycles=5

Here "data.mtz" is your reflection data file. PHENIX automatically
recognizes most of the known file formats, so it can be MTZ, CNS or ...

This will do the following:

1) Rigid body refinement first cycle only (MZ protocol = VERY high
convergence radius);
2) Refinement of individual xyz and b-factors every cycle with optimized
weights;
3) Simulated annealing at 2nd and one before the last cycles;

If this does not help, you need to start thinking -:)

For more info or if you have any questions: write me or look here:
http://www.phenix-online.org/

Cheers,
Pavel.

yang li wrote:
> Dear All,
> I have a 3A structure, the quality of the data is not very good.
> Now I have refined it to Rfree=40.7 in Refmac.
> But it wonnot go further down. Then I used CNS to do annealing, then
> use refmac to do rigid body refinement.
> The Rfree converged to 0.34, but if I use restrain refinement it will
> go up gradually. Then I use CNS refine
> script to refine the anneal.pdb, then the rigid body of refmac
> refinement converged at Rfree=0.33, but the refmac restrain
> refinement will still increase the Rfree--given weighting=0.03, after
> 80 cycle Rfree is 0.38 and seems like still increasing.
> Then I gave weighting=0.02, after 180 cycle, the Rfree is 0.37. I very
> wonder if I give 1000 cycle to run, Rfree
> will go back to 0.4. Can anybody give me some suggestions?
> By the way, it is a dimer and I didnot use NCS restarin during
> refinement. Below is from refmac log:
> Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
> $$
> 0 0.303 0.326 0.738 81869.2 0.012 1.575
> 0.104
> 1 0.288 0.337 0.722 81411.2 0.013 1.321
> 0.080
> 2 0.284 0.343 0.717 81312.9 0.011 1.303
> 0.081
> 3 0.282 0.347 0.713 81308.2 0.010 1.312
> 0.083
> 4 0.282 0.349 0.710 81326.4 0.010 1.313
> 0.083
> 5 0.281 0.352 0.708 81339.9 0.010 1.321
> 0.084
> 6 0.280 0.353 0.707 81356.4 0.010 1.322
> 0.085
> 7 0.280 0.355 0.705 81380.9 0.010 1.332
> 0.086
> 8 0.280 0.355 0.704 81390.5 0.010 1.330
> 0.086
> 9 0.279 0.359 0.702 81400.6 0.010 1.342
> 0.087
> 10 0.279 0.357 0.701 81405.1 0.010 1.340
> 0.086
> 11 0.279 0.360 0.700 81435.3 0.010 1.349
> 0.087
> 12 0.278 0.358 0.700 81425.8 0.011 1.363
> 0.086
> 13 0.278 0.362 0.698 81436.3 0.010 1.352
> 0.087
> 14 0.278 0.361 0.698 81438.1 0.010 1.347
> 0.086
> 15 0.278 0.364 0.696 81456.5 0.010 1.354
> 0.087
> 16 0.277 0.363 0.696 81452.3 0.011 1.352
> 0.087
> 17 0.278 0.365 0.695 81456.7 0.010 1.356
> 0.087
> 18 0.277 0.363 0.695 81450.3 0.011 1.348
> 0.087
> 19 0.277 0.366 0.694 81447.6 0.010 1.355
> 0.087
> 20 0.276 0.364 0.694 81448.2 0.011 1.350
> 0.087
> 21 0.277 0.366 0.693 81451.4 0.010 1.355
> 0.087
> 22 0.276 0.364 0.694 81442.4 0.011 1.350
> 0.087
> 23 0.277 0.366 0.693 81440.8 0.010 1.354
> 0.087
> 24 0.276 0.364 0.693 81434.4 0.011 1.350
> 0.087
> 25 0.277 0.365 0.693 81453.9 0.010 1.356
> 0.087
> 26 0.276 0.363 0.693 81446.5 0.011 1.352
> 0.087
> 27 0.276 0.365 0.693 81448.6 0.010 1.356
> 0.087
> 28 0.276 0.363 0.693 81438.2 0.011 1.352
> 0.087
> 29 0.276 0.364 0.693 81433.7 0.010 1.356
> 0.088
> 30 0.276 0.362 0.693 81430.1 0.011 1.352
> 0.087
> 31 0.276 0.364 0.692 81427.0 0.010 1.355
> 0.087
> 32 0.275 0.362 0.693 81421.2 0.011 1.354
> 0.087
> 33 0.276 0.364 0.692 81428.6 0.010 1.356
> 0.087
> 34 0.275 0.362 0.692 81421.9 0.011 1.355
> 0.087
> 35 0.275 0.364 0.691 81439.0 0.010 1.358
> 0.087
> 36 0.275 0.362 0.691 81435.9 0.011 1.356
> 0.087
> 37 0.275 0.364 0.691 81446.4 0.010 1.360
> 0.088
> 38 0.275 0.362 0.691 81444.6 0.010 1.358
> 0.087
> 39 0.275 0.364 0.690 81453.3 0.010 1.361
> 0.088
> 40 0.275 0.362 0.691 81443.5 0.010 1.360
> 0.087
> 41 0.275 0.363 0.690 81453.2 0.010 1.362
> 0.088
> 42 0.274 0.362 0.691 81443.8 0.010 1.361
> 0.088
> 43 0.275 0.364 0.690 81468.1 0.010 1.364
> 0.088
> 44 0.274 0.362 0.690 81471.5 0.010 1.363
> 0.088
> 45 0.274 0.364 0.689 81509.4 0.010 1.366
> 0.088
> 46 0.274 0.363 0.689 81498.1 0.010 1.364
> 0.088
> 47 0.274 0.364 0.689 81512.9 0.010 1.368
> 0.088
> 48 0.274 0.363 0.689 81499.2 0.010 1.366
> 0.088
> 49 0.274 0.365 0.688 81513.6 0.010 1.369
> 0.088
> 50 0.274 0.363 0.689 81509.3 0.010 1.368
> 0.088
> 51 0.274 0.365 0.688 81505.7 0.010 1.372
> 0.088
> 52 0.274 0.363 0.689 81498.6 0.010 1.370
> 0.088
> 53 0.274 0.365 0.688 81499.5 0.010 1.374
> 0.088
> 54 0.273 0.363 0.689 81488.1 0.010 1.372
> 0.088
> 55 0.273 0.365 0.688 81490.0 0.010 1.375
> 0.089
> 56 0.273 0.364 0.688 81495.7 0.010 1.374
> 0.088
> 57 0.273 0.365 0.688 81494.9 0.010 1.377
> 0.089
> 58 0.273 0.365 0.688 81476.1 0.010 1.376
> 0.089
> 59 0.273 0.366 0.687 81496.9 0.010 1.378
> 0.089
> 60 0.273 0.365 0.688 81496.1 0.010 1.376
> 0.089
> 61 0.273 0.367 0.687 81494.6 0.010 1.378
> 0.089
> 62 0.273 0.365 0.688 81480.5 0.010 1.377
> 0.089
> 63 0.273 0.367 0.687 81486.5 0.010 1.379
> 0.090
> 64 0.273 0.366 0.687 81483.1 0.010 1.378
> 0.090
> 65 0.273 0.367 0.687 81483.9 0.010 1.380
> 0.090
> 66 0.273 0.366 0.687 81479.1 0.010 1.378
> 0.090
> 67 0.273 0.367 0.687 81479.6 0.010 1.380
> 0.090
> 68 0.273 0.366 0.687 81479.4 0.010 1.379
> 0.090
> 69 0.273 0.367 0.687 81480.1 0.010 1.381
> 0.090
> 70 0.273 0.367 0.687 81489.5 0.010 1.379
> 0.090
> 71 0.273 0.368 0.687 81492.0 0.010 1.381
> 0.090
> 72 0.273 0.367 0.687 81486.0 0.010 1.379
> 0.090
> 73 0.273 0.368 0.687 81483.4 0.010 1.381
> 0.090
> 74 0.273 0.366 0.687 81479.5 0.010 1.379
> 0.090
> 75 0.273 0.367 0.687 81483.7 0.010 1.382
> 0.090
> 76 0.273 0.366 0.687 81486.5 0.010 1.380
> 0.090
> 77 0.273 0.367 0.686 81487.8 0.010 1.381
> 0.090
> 78 0.273 0.367 0.687 81494.2 0.010 1.380
> 0.090
> 79 0.273 0.368 0.686 81498.2 0.010 1.381
> 0.090
> 80 0.274 0.367 0.686 81499.0 0.010 1.379
> 0.090
> 81 0.274 0.368 0.686 81492.4 0.010 1.382
> 0.091
> 82 0.274 0.367 0.687 81493.9 0.010 1.381
> 0.090
> 83 0.274 0.368 0.686 81508.0 0.010 1.381
> 0.091
> 84 0.274 0.367 0.687 81505.1 0.010 1.381
> 0.091
> 85 0.274 0.369 0.686 81505.6 0.010 1.381
> 0.091
> 86 0.274 0.367 0.687 81504.1 0.010 1.381
> 0.091
> 87 0.274 0.369 0.686 81507.0 0.010 1.380
> 0.091
> 88 0.274 0.367 0.687 81506.4 0.010 1.382
> 0.091
> 89 0.273 0.369 0.686 81509.2 0.010 1.380
> 0.091
> 90 0.274 0.367 0.687 81506.5 0.010 1.381
> 0.091
> 91 0.274 0.369 0.686 81510.8 0.010 1.379
> 0.091
> 92 0.274 0.367 0.687 81516.3 0.010 1.380
> 0.091
> 93 0.273 0.369 0.687 81511.2 0.010 1.380
> 0.091
> 94 0.273 0.367 0.687 81502.3 0.010 1.380
> 0.091
> 95 0.273 0.369 0.686 81508.2 0.010 1.380
> 0.091
> 96 0.274 0.367 0.687 81508.7 0.010 1.380
> 0.091
> 97 0.273 0.369 0.687 81507.3 0.010 1.379
> 0.091
> 98 0.273 0.367 0.687 81506.2 0.010 1.379
> 0.091
> 99 0.273 0.369 0.687 81506.3 0.010 1.379
> 0.091
> 100 0.273 0.367 0.687 81511.4 0.010 1.379
> 0.091
> 101 0.273 0.369 0.687 81519.2 0.010 1.379
> 0.091
> 102 0.273 0.367 0.687 81514.9 0.010 1.380
> 0.091
> 103 0.273 0.369 0.687 81510.1 0.010 1.379
> 0.091
> 104 0.273 0.367 0.687 81504.4 0.010 1.380
> 0.091
> 105 0.273 0.369 0.687 81519.7 0.010 1.380
> 0.091
> 106 0.273 0.367 0.687 81505.1 0.010 1.379
> 0.091
> 107 0.273 0.369 0.687 81522.2 0.010 1.379
> 0.091
> 108 0.273 0.367 0.687 81503.6 0.010 1.379
> 0.091
> 109 0.273 0.369 0.687 81516.1 0.010 1.379
> 0.091
> 110 0.273 0.367 0.687 81507.9 0.010 1.379
> 0.091
> 111 0.273 0.369 0.687 81514.9 0.010 1.379
> 0.091
> 112 0.273 0.367 0.688 81502.1 0.010 1.379
> 0.091
> 113 0.273 0.368 0.687 81505.8 0.010 1.379
> 0.091
> 114 0.273 0.367 0.687 81507.0 0.010 1.380
> 0.091
> 115 0.273 0.369 0.687 81512.7 0.010 1.379
> 0.091
> 116 0.273 0.367 0.688 81504.4 0.010 1.380
> 0.091
> 117 0.273 0.368 0.687 81512.0 0.010 1.379
> 0.091
> 118 0.273 0.368 0.688 81512.5 0.010 1.379
> 0.090
> 119 0.273 0.369 0.687 81514.2 0.010 1.378
> 0.091
> 120 0.273 0.368 0.688 81518.6 0.010 1.379
> 0.090
> 121 0.273 0.369 0.687 81520.0 0.010 1.378
> 0.090
> 122 0.273 0.368 0.688 81524.6 0.010 1.379
> 0.090
> 123 0.273 0.369 0.687 81522.5 0.010 1.377
> 0.090
> 124 0.273 0.368 0.688 81525.0 0.010 1.379
> 0.090
> 125 0.273 0.369 0.687 81511.2 0.010 1.378
> 0.090
> 126 0.273 0.368 0.688 81515.6 0.010 1.379
> 0.090
> 127 0.273 0.370 0.687 81511.5 0.010 1.378
> 0.090
> 128 0.273 0.369 0.687 81520.6 0.010 1.380
> 0.090
> 129 0.273 0.370 0.687 81522.1 0.010 1.377
> 0.089
> 130 0.273 0.369 0.687 81525.5 0.010 1.374
> 0.088
> 131 0.273 0.370 0.686 81528.8 0.010 1.372
> 0.088
> 132 0.273 0.369 0.687 81528.9 0.010 1.371
> 0.088
> 133 0.273 0.370 0.686 81524.1 0.010 1.370
> 0.088
> 134 0.273 0.369 0.687 81527.9 0.010 1.371
> 0.088
> 135 0.273 0.371 0.686 81535.6 0.010 1.370
> 0.088
> 136 0.273 0.370 0.686 81536.0 0.010 1.370
> 0.088
> 137 0.273 0.371 0.686 81530.4 0.010 1.369
> 0.088
> 138 0.273 0.370 0.686 81532.5 0.010 1.369
> 0.088
> 139 0.273 0.371 0.686 81531.8 0.010 1.368
> 0.088
> 140 0.273 0.370 0.686 81527.9 0.010 1.369
> 0.088
> 141 0.273 0.371 0.686 81530.8 0.010 1.369
> 0.088
> 142 0.273 0.370 0.686 81522.6 0.010 1.370
> 0.088
> 143 0.273 0.372 0.685 81524.6 0.010 1.369
> 0.088
> 144 0.273 0.370 0.686 81514.4 0.010 1.370
> 0.088
> 145 0.273 0.372 0.685 81528.9 0.010 1.370
> 0.088
> 146 0.273 0.370 0.686 81515.6 0.010 1.370
> 0.088
> 147 0.273 0.372 0.685 81524.7 0.010 1.369
> 0.088
> 148 0.273 0.370 0.686 81522.6 0.010 1.370
> 0.088
> 149 0.273 0.372 0.685 81531.6 0.010 1.369
> 0.088
> 150 0.273 0.370 0.686 81519.6 0.010 1.370
> 0.088
> 151 0.273 0.372 0.685 81536.0 0.010 1.369
> 0.088
> 152 0.273 0.370 0.686 81527.7 0.010 1.370
> 0.088
> 153 0.273 0.371 0.685 81536.1 0.010 1.369
> 0.088
> 154 0.273 0.370 0.686 81526.6 0.010 1.371
> 0.088
> 155 0.273 0.371 0.685 81531.2 0.010 1.370
> 0.088
> 156 0.273 0.370 0.686 81523.3 0.010 1.370
> 0.088
> 157 0.273 0.370 0.685 81518.6 0.010 1.370
> 0.088
> 158 0.273 0.369 0.686 81516.9 0.010 1.372
> 0.088
> 159 0.273 0.370 0.685 81523.8 0.010 1.370
> 0.088
> 160 0.273 0.369 0.686 81512.8 0.010 1.371
> 0.088
> 161 0.273 0.370 0.685 81514.7 0.010 1.370
> 0.088
> 162 0.273 0.369 0.685 81515.2 0.010 1.368
> 0.088
> 163 0.273 0.371 0.685 81525.4 0.010 1.370
> 0.088
> 164 0.273 0.369 0.685 81508.3 0.010 1.369
> 0.088
> 165 0.273 0.371 0.684 81522.5 0.010 1.370
> 0.088
> 166 0.273 0.369 0.685 81525.8 0.010 1.368
> 0.088
> 167 0.273 0.371 0.684 81531.7 0.010 1.371
> 0.088
> 168 0.273 0.369 0.684 81534.7 0.010 1.369
> 0.088
> 169 0.273 0.371 0.684 81537.8 0.010 1.371
> 0.088
> 170 0.273 0.370 0.684 81534.8 0.010 1.369
> 0.088
> 171 0.273 0.371 0.683 81552.7 0.011 1.372
> 0.088
> 172 0.273 0.370 0.683 81552.5 0.010 1.370
> 0.088
> 173 0.273 0.371 0.683 81552.1 0.010 1.372
> 0.088
> 174 0.273 0.370 0.683 81545.7 0.010 1.370
> 0.088
> 175 0.273 0.371 0.683 81556.1 0.010 1.373
> 0.088
> 176 0.273 0.370 0.683 81560.3 0.010 1.371
> 0.088
> 177 0.273 0.371 0.682 81568.8 0.010 1.372
> 0.088
> 178 0.273 0.370 0.683 81567.8 0.010 1.371
> 0.088
> 179 0.273 0.371 0.682 81568.0 0.010 1.374
> 0.088
> 180 0.273 0.370 0.683 81565.7 0.010 1.372
> 0.088
>

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008

Previous message:
Subject: cns and refmac refinement
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-02-21

Next message:
Subject: Re: Vista
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-21